At Crooked Timber they're having a discussion of "top" political philosophy books of the last decade. I don't know what the "top" IR books of the decade (meaning, here, 2000 and forward) are, but I thought I'd throw out the names of some possible candidates. The list is biased by what happens to be on my bookshelf or in my head at the moment and by my own particular interests. In a few cases, to be noted, I haven't read a word of the books in question, so those instances represent just hunches that the book is worth reading. The list is arranged by date of publication (earliest first).
Robert Jackson, The Global Covenant (2000). Aims to integrate the "political theory of human conduct" (identified by the author with Oakeshott, Collingwood, and Berlin) and the international society tradition, especially its more conservative, pluralist side. A vigorous normative defense of the traditional principles of non-intervention and state sovereignty.
Joshua Goldstein, War and Gender (2001). Argues that societies throughout history have molded men to be warriors and slotted women primarily into supporting rather than combat roles, even though some women are as physically capable of being soldiers as men (or in some cases, more capable). In other words, while there are average physical differences between the sexes, culture is more constraining than biology or anatomy. The book is a sweeping multidisciplinary synthesis. (For critical comment, see the review symposium in Perspectives on Politics; I'm too lazy to get the citation right now.) [Disclosure alert: I know the author.]
John Mearsheimer, The Tragedy of Great Power Politics (2001). I disagree with this book's argument and perspective, but it's a major statement by a noted scholar. And he writes well.
Thomas Pogge, World Poverty and Human Rights (2002). In contrast for example to Jackson's The Global Covenant, Pogge argues that some basic institutional aspects of the global order are unjust and that "the citizens and governments of the wealthy societies, by imposing the present global economic order, significantly contribute to the persistence of severe poverty and thus share institutional moral responsibility for it." He makes some specific proposals, e.g. for "a global resources dividend."
Peter Katzenstein, A World of Regions: Asia and Europe in the American Imperium (2005). Bought it but have not read it.
Stephen Walt, Taming American Power (2005). Insightful analysis of "the global response to U.S. primacy" (to quote the subtitle).
Patrick T. Jackson, Civilizing the Enemy: German Reconstruction and the Invention of the West (2006). Have not read it but am familiar with some of the author's articles (and also [disclosure alert] know the author).
Saskia Sassen, Territory, Authority, Rights: From Medieval to Global Assemblages (2006). Bought it but have read only a tiny bit of it. I suspect, however, that Sassen is stronger on the "global" than the "medieval" part of her subject.
Lawrence Wright, The Looming Tower: Al-Qaeda and the Road to 9/11 (2006). The only book on this list by a journalist rather than an academic, but it's researched with scholarly thoroughness. Very good on the background of bin Laden and Zawahiri; the portrait of the latter is especially revealing.
Alexander Downes, Targeting Civilians in War (2008). After dipping into parts of this book, I'm not sure I entirely agree with the argument; however, it's a thoughtful and well-researched approach to the topic.
George Gavrilis, The Dynamics of Interstate Boundaries (2008). Have not read it, but anyone with a serious interest in this subject will want to.
Daniel Nexon, The Struggle for Power in Early Modern Europe (2009). My bookmark is stuck at p.126 and may remain there permanently. Contains interesting ideas, but the exposition in the theoretical chapters could have been tightened and shortened.
George Quester, Preemption, Prevention and Proliferation: The Threat and Use of Weapons in History (2009). A short book by a well-known scholar. I have only dipped into it.
There are other titles I could mention but I'll stop here, at least for now. Comments, suggestions, criticisms? Chime in.